From lim@rani.chem.yale.edu  Fri Feb 11 00:21:27 1994
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From: Dongchul Lim <lim@rani.chem.yale.edu>
Message-Id: <9402110430.AA08218@rani.chem.yale.edu>
Subject: Re: religious debate
To: chemistry@ccl.net (Computational Chemistry)
Date: Thu, 10 Feb 94 23:30:32 EST
In-Reply-To: <9402110209.AA25216@neon.chem.utk.edu>; from "Edward Wolpert" at Feb 10, 94 9:09 pm
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=== One more bomb to the battle field ===
The question of which language is the best depends on what you
want to do with it and how experienced you and your colleagues
are with that language.
If the majority of members in a group are familiar with a
particular language, it'll be much more effective to do a co-work
with that language, unless it has tremendous deficiencies.
Likewise, if you're very familiar with one language, there are
not many reasons to code in other languages.
Objected-oriented, graphics, or operating system-related programs
can be written more efficiently with C or object-oriented languages
such as SmallTalk and C++.
But if you're going to write a simple number crunching program
such as Huckel Theory, you'll never need C++.
You could do it with fortran, basic, perl, awk... Maybe even
with Korn shell script. Or maybe with Texas Instrument calculator.
-D


From mw@crystal.uwa.edu.au  Fri Feb 11 04:21:33 1994
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From: mw@crystal.uwa.edu.au (Magda Wajrak)
Message-Id: <9402110846.AA07675@pack.crystal.uwa.edu.au>
Subject: Ir spectra of...?
To: chemistry@ccl.net
Date: Fri, 11 Feb 94 16:46:07 WST
Mailer: Elm [revision: 70.85]


Dear Netters,

I am desperately trying to find i.r. spectra of the following compounds.
I have done a thorough literature search, but I am worried that I might 
have missed something. I any one knows of any references which might have
the spectra of any of these compounds I would appreciate their help.

Thank you very much


1.	1,2-Bis(F-alkyl)cyclo-1,2-diaza-3,4,5,6-tetrasulfanes, RfN-S4-NRf

2.	S4(NH)2,   Tetrasulfur Diimide


Magda Wajrak
(PhD student)

mw@crystal.uwa.edu.au

From tgtatj@chem.tue.nl  Fri Feb 11 06:22:20 1994
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Subject: postdoc Cray Research Grant
To: chemistry@ccl.net
Date: Fri, 11 Feb 1994 12:03:14 +0100 (MET)
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The Theory-group of the Laboratory for Inorganic Chemistry and Catalysis
at the Eindhoven University of Technology has at the moment a vacancy
for a

     POSTDOC

for one year. The postdoc will work in the

     HIGH-DIMENSIONAL QUANTUM DYNAMICS

project. In this project quantum effects in the reactions of small
molecules on simple surfaces of transition metals are studied. Using grid
methods the time-dependent Schroedinger-equation is solved. The
wavefunction is written as a sum of products of single-particle
functions. This leads to the multi-configuration time-dependent
Hartree-method (MCTDH).[1,2] The Schroedinger-equation is replaced by a
set of equations of motion for the single-particle functions. In general
it is only possible to do 1D, 2D, and 3D studies when you try to solve
the Schroedinger-equation directly. MCTDH makes it possible to study
systems with more degrees of freedom. The implementation of MCTDH used
in Eindhoven uses object-oriented programming (C++). Test have been done
on a 2D model of the H2 dissociation on copper. At the moment the
dissociation of CH4 on nickel is studied (3D and 4D models). Other
reactions of interest are the CO oxidation on various transition metals
(5D), the scattering of linear molecules from surfaces (5D), and
higher-dimensional models of H2 dissociation.  The project is
financed by the Netherlands Organization for National Computer
Facilities (NCF) via a Cray Research University Grant. The position is
to be filled as soon as possible. For more information and applications
contact

     Dr. A.P.J. Jansen
     T/TAK, TUE
     P.O. Box 513
     5600 MB  Eindhoven
     The Netherlands
     tel.: (040) 47 50 37
     fax.: (040) 45 50 54
     Email: tgtatj@chem.tue.nl

References:
[1] U. Manthe, H.-D. Meyer, and L.S. Cederbaum
    J.Chem.Phys. 97 (1992) 3199.
[2] A.P.J. Jansen,
    J.Chem.Phys. 99 (1993) 4055.

From reinert@VAX.MPIZ-KOELN.MPG.d400.de  Fri Feb 11 08:21:56 1994
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To: chemistry@ccl.net
Subject: FOLDER?


Dear fellow netters,

I am interested in the Homology Modeling program FOLDER. I have e-mailed 
S.Srinivasan (one of the authors) but did not get a reply. 
Can anybody tell me where to get this software, please?

Many thanks in advance!


			Peter Reinert


Peter Reinert (ZWDV), Max-Planck-Institut fuer Zuechtungsforschung,
Carl-von-Linne-Weg 10, 50829 Koeln, Germany
Phone: ++49/221/5062-539 or -538 or -537, FAX: ++49/221/5062-513
"reinert@vax.mpiz-koeln.mpg.d400.de"

From fredvc@esvax.dnet.dupont.com Fri Feb 11 08:29:43 1994
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Date: Fri, 11 Feb 94 08:29:39 EST
To: wolpert@neon.chem.utk.edu
Cc: mail11:esvax::;@ccl.net (@dis:chem), fredvc@esvax.dnet.dupont.com
To: chemistry@ccl.net, wolpert@neon.chem.utk.edu
Subject: CCL: religious debate 



I usually avoid consuming band width for computational theology (e.g., FORTRAN
vs. C; Vector-parallel vs. scalable PP; etc.) but a recent posting needs a
response, if only to provide a alternate perspective to the "young" readers of
this list.

Edward Volpert writes:

>>	Much of what is written for computers currently is in C or C++.  
>>Yet banks still use Cobol, and Fortran is popular with chemistist.  
>>To be honest, those aren't that readable... you have to train yourself
>>to understand what is going on.  In C, you can write some really bone-head
>>statements.  C++ restricts you somewhat, but if you wanted, you stil can
>>write unreadable code.  

FREDVC:	It is true that you can write incomprehensible code in ANY language.
	However, having just gone through a self-tutorial in C, I consider
	it to be MUCH EASIER to do so in C!!.

>>                   IMHO, it's hard to really optimize fortran code, and
>>the compilers out there can't do it as well as someone can opt C code.
>>If someone wanted to try to re-write HONDO in C, I believe it would run
>>faster.

FREDVC:	I have a problem with parts of this.  

    (a)	I don't consider it to be that hard to optimize FORTRAN.  (I began to
	worry about this 9-10 years ago in a serious way, when our first CRAY 
	came in.)  What I have consistently found is that there are some good 
	programming practices which, if adhered to scrupulously, provide 
	improved performance on a wide variety of platforms including vector 
	machines.  Perhaps your view is shaped by being more experienced in C 
	than in FORTRAN.

    (b) FORTRAN compilers are pretty sophisticated these days.  I am told, in 
	fact, that todays best compilers can beat hand-optimized assembler
	code in many instances.  If this is true, there may not be as much of
	a "C advantage" as one might think.  I have done some simple kernels on 
	a CRAY Y-MP in both C & FORTRAN, and their execution speeds are the 
	same within "experimental error".  It may well be, however, that CRAY
	Research, Inc., has put special effort into insuring "comparability".

>>	Now the real question: Who wants to try that?
>>This debate will not end until someone does just that. Period. When you can
>>compare real applications that are as intensive as HONDO, then well have
>>facts about the best programming lang, not just emotions.  Of course, then
>>we could always try APL for HONDO, perhaps that's faster?  Nahhh...

FREDVC:	This is not as simple as it looks:  (1) Which version of HONDO do we
	use as a reference point, GAMESS-87, GAMESS-92, GAMESS-UK??  (2) Do we
	compare to the FORTRAN code as it stands, or do we allow for its 
	optimization as well??  Do we optimize for a vector-parallel platform 
	or a scalable parallel-processing platform??  etc.

	No criticism is intended; I just want to highlight that this is not
	as simple an issue as it would appear at first glance.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
                           FREDERIC A. VAN-CATLEDGE

Scientific Computing Division         ||   Office: (302) 695-1187 or 529-2076
Central Research & Development Dept.  ||          
The DuPont Company                    ||      FAX: (302) 695-9658
P. O. Box 80320                       ||
Wilmington DE 19880-0320              || Internet: fredvc@esvax.dnet.dupont.com 
--------------------------------------------------------------------------------
Opinions expressed in this electronic message should ***> NOT <*** be taken to 
represent the official position(s) of the DuPont Company.  

*****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <*****
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From hogue@canada.den.mmc.com  Fri Feb 11 11:21:51 1994
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From: hogue@canada.den.mmc.com (Pat Hogue 1-2183)
Message-Id: <9402111534.AA08901@canada.den.mmc.com>
To: chemistry@ccl.net
Subject: Satellite video 


Does anyone know if the ACS satellite presentation for March 29th
entitled "Molecular Modeling: The Small-Molecule Approach
(Success Stories)" is being offerred anywhere in the Denver or
Front Range region?  It appears as though CSM, CSU and CU are 
not goint to participate.  The cost per site of $2200 or cost
 per head of $200 is not a little high for aerospace folks.

Pat Hogue 

From raman@bioc01.uthscsa.edu  Fri Feb 11 11:28:26 1994
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From: raman@bioc01.uthscsa.edu (C.S.RAMAN)
Message-Id: <9402111543.AA29246@bioc01.uthscsa.edu>
Subject: Re: CCL:FOLDER?
To: reinert@VAX.MPIZ-KOELN.MPG.d400.de
Date: Fri, 11 Feb 1994 09:43:55 -0600 (CST)
Cc: chemistry@ccl.net
In-Reply-To: <12*/S=reinert/OU=VAX/O=MPIZ-KOELN/PRMD=MPG/ADMD=d400/C=de/@MHS> from "reinert@VAX.MPIZ-KOELN.MPG.d400.de" at Feb 11, 94 04:13:34 pm
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> I am interested in the Homology Modeling program FOLDER. I have e-mailed 
> S.Srinivasan (one of the authors) but did not get a reply. 
> Can anybody tell me where to get this software, please?

I communicated with the authors in early December and was told that the
program hasn't reached a stage where it can be distributed.  I believe
they are trying to find a way to do the same.  If I hear anything more,
I will pass the information along.  In the meanwhile, you can try a
program called PROMOD, which essentially does homology modelling and is
available free of charge (just the object code).

Cheers
-raman
-- 
C.S.Raman                                 raman@bioc01.uthscsa.edu - Internet
UNIX Programming & Administration         70412.2354@compuserve.com - CIS
SPARC & SGI Systems                       raman@hermes.chpc.utexas.edu - CHPC
Department of Biochemistry                c.raman@launchpad.unc.edu
UTHSCSA       
7703 Floyd Curl Dr.                       (210) 567-6623   [Tel]
San Antonio, TX 78284-7760                (210) 567-6595   [Fax]
******************************************************************************
         If a man's wit be wandering, let him study the Mathematics
                                                            -Francis Bacon   
******************************************************************************

From h.rzepa@ic.ac.uk  Fri Feb 11 13:21:38 1994
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Date: Fri, 11 Feb 1994 17:43:45 +0000
To: CHEMISTRY@ccl.net
From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa)
Subject: Chemistry MIME types.


Along with increasing use of world wide webb information browsers
comes a recognition that we need to use "live" chemical information,
not just pretty "bitmap" images. The content of any particular file is
defined by its "MIME type". Hence these can be text, image,
audio, video, application etc etc. There are in fact 7 primary types.
Under this there are sub-sets, for example
application/word to indicate a word document etc. It struck me that we
need perhaps an 8th type, for chemistry. For example;

chemistry/pdb
chemistry/csd
chemistry/cif

etc etc. The user would associate each with their favourite "viewer",
ideally capable of picking up  the qualifier and treating it accordingly.
One might even one day get intelligent e-mail programs that would convert
the chemical mime type into an on-screen structure, embedded amongst
the text etc.

I sent this suggestion to Nathaniel Borenstein, one of the two (?) global
coordinators of the MIME initiative, and received a highly enthusiastic
response for the general concept. However, he urged the community to
prepare an Internet discussion document to thrash out the detail. To
provide material for such a document, I now solicit the net. But keep it
short please!


Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY;
rzepa@ic.ac.uk via Eudora 2.01, Tel:+44  71 225 8339, Fax:+44 71 589 3869.
>From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804
http://www.ch.ic.ac.uk/rzepa.html




From eslone@mason1.gmu.edu  Fri Feb 11 13:26:35 1994
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Subject: Nomenclature Programs
To: chemistry@ccl.net
Date: Fri, 11 Feb 1994 12:38:30 -0500 (EST)
From: "J. Eric Slone" <eslone@mason1.gmu.edu>
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Dear Netters:


Here is the information on the responses I received for a program to 
translate an IUPAC name to a structure.  I appreciate all of the response 
I received on this query.  

I have uploaded a Mac program called IUPAC.SIT to the ccl.net archives.
This program came from Compuserve and is currently in the /incoming
directory.  I'm not sure where it will end up once it's moved.  Since I
don't have a Mac, and have no way to play with it, I can't provide any
comments on it.  

For Windows, there is a program which many people wrote to me about, and
was mentioned in last week's C&EN called ChemNameStru.  It's available
>from ChemInnovation Software, (619) 566-2846, San Diego, CA, USA.  Their
literature posts a price of $149, academic $129, "regular price" $249.

There is also a DOS program which was mentioned in many of the messages, 
but I don't have any contact information.  The price is somewhere 
around $300.

What I'd really like to see someday is a program that can take a
structure as input and generate a name for it.  Perhaps even have a
database of trivial names and display those also.  I don't suppose any
of the people out there involved in the "religious" discussion about
programming languages would care to tackle this one?

Just to put in my 10 cents on that topic, when I was working as a
programmer, I wrote code in Basic, Cobol, Pascal, Fortran, and C.  I
have to say, C was the best of the languages (in my humble opinion).

Thanks again to all who responded,

Eric


PS:  Does anyone have a free/shareware program to translate to/from
     SMILES notation?

________________________________________________________________________________

 J. Eric Slone                         Scientific Consulting Services
                                       Serving Government & Industry Since 1982
 Internet:   eslone@mason1.gmu.edu
 Compuserve: 73757,2776                "True science teaches, above all, to
 Fax:        (703) 751-6639             doubt, and to be ignorant."
 Voice:      (703) 461-7078                               Miguel do Unamuno
________________________________________________________________________________





From WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU  Fri Feb 11 14:21:38 1994
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 11 Feb 1994 13:45:47 EST
Date: Fri, 11 Feb 1994 13:45:47 -0500 (EST)
Subject: Software expiration ethics
To: chemistry@ccl.net
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Hello netters,

	I would like to raise an ethical question with repect to
self-expiring software, that is, software which no longer functions after
a certain time.

1) If the software has an expiration date, that fact should be mentioned up
front.  This applies to free software, too.  The user has a right to know
if his "free" software will suddenly quite working.  For commercial
software, expiration dates (if any) should be disclosed on any price
list.

2) Commercial (i.e., not free) software which has an expiration date should
never be offered for "purchase".  It always should be offered for "lease"
for the specified time period.

	I am interested in your reaction to these points, or any related
points that are relevant.

Don Williams
dewill01@ulkyvx.louisville.edu

From DSMITH@uoft02.utoledo.edu  Fri Feb 11 15:21:44 1994
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Date: Fri, 11 Feb 1994 15:05:59 -0500 (EST)
From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" <DSMITH@uoft02.utoledo.edu>
Subject: Re: CCL:Nomenclature Programs
To: eslone@mason1.gmu.edu
Cc: chemistry@ccl.net
Message-id: <01H8RHSPMXLU000UOJ@UOFT02.UTOLEDO.EDU>
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There is already a program that can take a structure and generate a name
>from the graphical input.  It is called Autonom, and was developed and
is maintained by the folks at the Beilstein Institute.  It runs on a PC and
I believe a VAX.  For a software review, see:

Smith, D. A. J. Am. Chem. Soc. 1992, 114, 10680-1.

For articles describing the algorithms, see:

Goebels, L; Lawson, A. J.; Wisniewski, J. L. J. Chem. Inf. Comput. Sci. 1991, 
31, 216.
Wisniewski, J. L. J. Chem. Inf. Comput. Sci. 1990, 30, 324.

The program is sold through Springer-Verlag, 175 Fifth Avenue, NY, NY
10010.  Voice:  212-460-1500.  Fax 212-473-6272.  The person who used to
be in charge and may still be was Barbara Lange.

Doug

Douglas A. Smith
Assistant Professor
Department of Chemistry
 and member,
Center for Drug Design and Development
The University of Toledo
Toledo, OH  43606-3390

voice    419-537-2116
fax      419-537-4033
email    dsmith@uoft02.utoledo.edu


From CHM001@marshall.wvnet.edu  Fri Feb 11 17:21:42 1994
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Date: Fri, 11 Feb 1994 17:00:57 -0500 (EST)
From: "DR. LAWRENCE R. SCHMITZ" <CHM001@marshall.wvnet.edu>
Subject: RE:thermochem in gaussian
To: chemistry@ccl.net
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Mike McAllister writes:
"Is there a reasonably straight forward way to get calculated
enthalpies from a gaussian frequency job??"

   My colleagues and I have been working on simple scheme to
calculate heats of formation from 6-31G* energies for several
years.  Our approach is to add an empirically determine set
of increments to the HF/6-31G* energy.  Once the increments
have been determined and the 6-31G* calculation done, the rest
of the calculation is simple (back of an envelope).  We have
published increment suitable for determining heats of formation
for a number of common functional groups as summarized below.

Alkenes. J. Comput. Chem., submitted.  (write to me if you
need these)

Alkyl Radicals. J. Phys. Org. Chem., 6, 551 (1993).

Thiols. Heteroatom Chem. 1992, 3, 69.

Acids and Esters. J. Comput. Chem.,  13, 838 (1992).

Aldehydes and Ketones. J. Phys. Org. Chem., 5, 225 (1992).

Alcohols and Ethers. J. Am. Chem. Soc., 114, 2880 (1992).

Alkanes and Aliphatic Amines. J. Phys. Org. Chem., 3, 732 (1990).


Larry


Larry Schmitz
Department of Chemistry
Marshall University
Huntington, WV 25755

CHM001@MARSHALL.WVNET.EDU

From jkl@ccl.net  Fri Feb 11 18:21:39 1994
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Date: Fri, 11 Feb 1994 17:36:28 -0500
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To: chemistry@ccl.net
Subject: Re:  Questions about MDL
Forwarding: Mail from '"Michele Meyers, Extension 1385" <MICHELE@mdli.com>'
     dated: Fri, 11 Feb 1994 08:02:18 -0800 (PST)
Cc: jkl@ccl.net


Forwarding a clarification to the list...
Jan, jkl@ccl.net

---------- Begin Forwarded Message ----------
>From MICHELE@mdli.com Fri Feb 11 11:44:46 1994
Date: Fri, 11 Feb 1994 08:02:18 -0800 (PST)
From: "Michele Meyers, Extension 1385" <MICHELE@mdli.com>
Subject: Re:  Questions about MDL
To: jkl@ccl.net


Patrick van der Valk (FS300627@Sol.YorkU.Ca) inquired:

>Hi there, 
>
>I am interested in obtaining the ISIS/DRAW & ISIS/BASE package.However, a
>couple of days ago someone told me that the company that supports this
>package (MDL) is in serious problems. Does anyone know more about this?
>Thanks.
----------  signature deleted -------

Your inquiry about the state of MDL was forwarded to me by a number
of MDL's partner companies.  I would like to reply briefly and encourage
you to contact us directly for more information.  

MDL is indeed alive and well here in San Leandro, CA.  We became a public
company back in July, 1993.  The information you may have heard about
financial difficulty stems from our former owners, Maxwell Communications,
being bankrupt.  MDL was one of the few profitable businesses owned
by this company and as such, we went public to earn money to pay off
the debtors of our parent.  As a new company with a new name, MDL is
strong financially, our products are being enhanced to deliver new
functionality, and you can count on long-term support from us for
any products you purchase.  We have been a profitable company for the
15 years we have been in business and continue strong now that we are
out from under the Maxwell umbrella.

I hope you feel more confident about purchasing MDL products.  Feel free
to contact me to ask more specific questions, or contact our telemarketing
group at 800 MDL 0064 for details on our products.  

Michele Meyers
Manager, Business Relationships
Third Party Marketing
MDL Information Systems, Inc.
michele@mdli.com
510 895-1313 x 1385
----------- End Forwarded Message -----------


From hogue@canada.den.mmc.com  Fri Feb 11 19:21:40 1994
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From: hogue@canada.den.mmc.com (Pat Hogue 1-2183)
Message-Id: <9402112344.AA09418@canada.den.mmc.com>
To: chemistry@ccl.net
Subject: Molecular Modeling TV Course


In my earlier post about the ACS TV course 
"Molecular Modeling: The Small Molecule Approach 
(Success Stories)" I forgot to mention that a 
description can be found in the January 24, 1994 
issue of Chemical and Engineering News.  The ACS 
phone number is 1-800-227-5558 or (202) 872-6124, 
their fax number is (202) 872-6336.  Hope this is 
helpful information.

Pat Hogue

From FS300627@Sol.YorkU.CA  Fri Feb 11 19:29:38 1994
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 <01H8RQ1V1MMS90SG3P@Sol.YorkU.CA>; Fri, 11 Feb 1994 18:56 EDT
Date: Fri, 11 Feb 1994 18:56 EDT
Subject: MDL: Alive 'n' Kicking
To: chemistry@ccl.net
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I would like to thank everybody who told me about MDL (or MDLi as it is
now called). I got several messages and phone calls from the people at
MDLi and they assured me that they are doing (very) well. So I appologize
if I caused unnecessary panic.

 **************************************************************************
** Patrick van der Valk         | It is a capital mistake to theorize     *
** BioMimic                     | before one has data. Insensibly one     *
**                              | begins to twist facts to suit theories  *
** e-mail:FS300627@Sol.YorkU.Ca | instead of theories to suit facts.      *
** Phone: (416) 739-0783        |                                         *
** Fax: (416) 650-3558          |                 -Sherlock Holmes-       *
 **************************************************************************


